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r488: parameter to control max fragment length

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This commit is contained in:
Heng Li
2017-10-07 23:54:32 -04:00
parent f150257a0d
commit 61e56c941d
3 changed files with 29 additions and 17 deletions
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main.c
+7 -7
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@@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r487-dirty"
#define MM_VERSION "2.2-r488-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -64,7 +64,7 @@ static inline int64_t mm_parse_num(const char *str)
int main(int argc, char *argv[])
{
const char *opt_str = "aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:h";
const char *opt_str = "aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:";
mm_mapopt_t opt;
mm_idxopt_t ipt;
int i, c, n_threads = 3, long_idx, max_gap_ref = 0;
@@ -98,6 +98,7 @@ int main(int argc, char *argv[])
else if (c == 'v') mm_verbose = atoi(optarg);
else if (c == 'g') opt.max_gap = (int)mm_parse_num(optarg);
else if (c == 'G') max_gap_ref = (int)mm_parse_num(optarg);
else if (c == 'F') opt.max_frag_len = (int)mm_parse_num(optarg);
else if (c == 'N') opt.best_n = atoi(optarg);
else if (c == 'p') opt.pri_ratio = atof(optarg);
else if (c == 'M') opt.mask_level = atof(optarg);
@@ -180,10 +181,8 @@ int main(int argc, char *argv[])
}
}
if (max_gap_ref > 0) {
if (opt.flag & MM_F_FRAG_MODE)
opt.max_gap_ref = max_gap_ref;
if (opt.flag & MM_F_SPLICE)
opt.max_gap_ref = opt.bw = max_gap_ref;
opt.max_gap_ref = max_gap_ref;
if (opt.flag & MM_F_SPLICE) opt.bw = max_gap_ref; // in the splice mode, this also changes the bandwidth
}
if ((opt.flag & MM_F_OUT_SAM) && (opt.flag & MM_F_OUT_CS_LONG)) {
opt.flag &= ~MM_F_OUT_CS_LONG;
@@ -203,7 +202,8 @@ int main(int argc, char *argv[])
fprintf(fp_help, " Mapping:\n");
fprintf(fp_help, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%g]\n", opt.mid_occ_frac);
fprintf(fp_help, " -g NUM stop chain enlongation if there are no minimizers in INT-bp [%d]\n", opt.max_gap);
fprintf(fp_help, " -G NUM max intron length (-x splice) [200k]; or insert size (-x sr) [1000] []\n");
fprintf(fp_help, " -G NUM max reference skip length [-xsplice:200k]\n");
fprintf(fp_help, " -F NUM max fragment length in the fragment mode [-xsr:800]\n");
fprintf(fp_help, " -r NUM bandwidth used in chaining and DP-based alignment [%d]\n", opt.bw);
fprintf(fp_help, " -n INT minimal number of minimizers on a chain [%d]\n", opt.min_cnt);
fprintf(fp_help, " -m INT minimal chaining score (matching bases minus log gap penalty) [%d]\n", opt.min_chain_score);